Antimicrobial Activity Screening of Rhizosphere Soil Bacteria from Tomato and Genome-Based Analysis of their Antimicrobial Biosynthetic Potential

Abstract

Background: Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking environment-friendly and cost-effective green methods in agricultural production becomes crucial nowadays. Plant Growth Promoting Rhizobacteria (PGPR) can promote plant growth through biological activity. Their use is considered to be a promising sustainable approach for crop growth. Moreover, a vast number of biosynthetic gene clusters (BGCs) for secondary metabolite production are being revealed in PGPR, which helps to find potential anti-microbial activities for tomato disease control.Results: We isolated 351 bacterial strains (181 of which are Bacillus sp.) from healthy tomato, rhizosphere soil, and tomato tissues. In vitro antagonistic assays revealed that 34 Bacillus strains have antimicrobial activity against Erwinia carotovora, Pseudomonas syringae; Rhizoctonia solani; Botrytis cinerea; Verticillium dahliae and Phytophthora infestans. The genomes of 10 Bacillus and Paenibacillus strains with good antagonistic activity were sequenced. Via genome mining approaches, we identified 120 BGCs encoding NRPs, PKs-NRPs, PKs, terpenes and bacteriocins, including known compounds such as fengycin, surfactin, bacillibactin, subtilin, etc. In addition, several novel BGCs were identified. We discovered that the NRPs and PKs-NRPs BGCs in Bacillus species are encoding highly conserved known compounds as well as various novel variants.Conclusions: This study highlights the great number of varieties of BGCs in Bacillus strains. These findings pave the road for future usage of Bacillus strains as biocontrol agents for tomato disease control and are a resource arsenal for novel antimicrobial discovery.

Genomic insights on fighting bacterial wilt by a novel Bacillus amyloliquefaciens strain Cas02

“…1 ). An important biocontrol mechanism of biological control agents (BCAs) involves the secretion of antibacterial substances and inhibition of pathogen growth (Zhou et al ., 2021 ). Among the top 10 bacterial species listed based on their scientific and economic importance in plant diseases, Pseudomonas syringae pathovars and Ralstonia solanacearum were ranked as the first and second most important bacterial pathogens respectively (Mansfield et al ., 2012 ).…”

Screening and Biocontrol Potential of Rhizobacteria Native to Gangetic Plains and Hilly Regions to Induce Systemic Resistance and Promote Plant Growth in Chilli against Bacterial Wilt Disease

“…Similar results were found, where a total of 180 strains of Bacillus were isolated from the tomato rhizosphere and these strains were tested against Pseudomonas syringae , Phytophthora infestans , Verticillium dahliae , Erwinia carotovora and Botrytis cinerea . Moreover, 34 Bacillus strains were found to have the best antagonistic activity against these plant pathogens with the production of surfactin, subtilin fengycin and bacillibactin compounds [ 82 ]. Ramesh and Phadke (2012) carried out a similar study in which they isolated 109 strains of endophytic rhizobacteria from eggplants and assessed their biocontrol efficiency against R. solanacearum [ 16 , 83 ].…”

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov

“…5B). Similarly, Zhou L et al found the great number of varieties of BGCs in Paenibacillus and Bacillus strains by genome mining [25].…”